Bump to v0.4.0, document context graph feature

- Bump version 0.3.3 → 0.4.0 (new feature, backward compatible)
- Document context_query, graph_annotate, session_summary tools in README
- Add graph configuration env vars to README
- Update project structure to include graph/ and tools/
- Update architecture.md with graph component details
- Add code-graph, context-graph keywords to package.json

Author: Ricoledan

README.md

@@ -26,6 +26,8 @@ Using local embeddings and vector search, it bridges the gap between text search
 ## Features
 
 - **Semantic search** - Find code by meaning, not just keywords
+- **Context graph** - Understand how code connects (calls, imports, inheritance) with graph-enhanced search
+- **Session memory** - Track agent exploration state across multi-turn conversations
 - **AST-aware chunking** - Tree-sitter WASM for cross-platform parsing, no native compilation required
 - **Local embeddings** - ONNX Runtime with nomic-embed-code (768 dims, 8K context)
 - **Hybrid search** - Vector similarity + BM25 keyword matching
@@ -127,14 +129,80 @@ semantic_search({
 ## Architecture
 
 ```
-semantic_search tool (MCP Server)
+MCP Server
 ├── Chunker (web-tree-sitter) → AST-aware code splitting (WASM, cross-platform)
 ├── Embedder (ONNX local)     → nomic-embed-code, 768 dims
 ├── Vector DB (LanceDB)       → Serverless, hybrid search
+├── Context Graph (SQLite)    → Structural relationships + session memory
 ├── File Watcher (chokidar)   → Incremental updates
 └── Hybrid Search             → BM25 + vector + reranking
 ```
 
+## Context Graph (Opt-in)
+
+The context graph adds structural awareness on top of semantic search. Enable it with:
+
+```bash
+SEMANTIC_CODE_GRAPH_ENABLED=true
+```
+
+When enabled, the server extracts structural relationships (calls, imports, extends, implements) from the AST during indexing and stores them in a SQLite graph. This powers three additional tools.
+
+### Tool: context_query
+
+Semantic search + graph neighborhood expansion. Returns search results enriched with structural context.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `query` | string | Yes | Natural language query |
+| `path` | string | No | Directory to scope the search |
+| `limit` | number | No | Maximum results (default: 10) |
+| `file_pattern` | string | No | Glob pattern to filter files |
+| `depth` | number | No | Graph traversal depth (1-3, default: 1) |
+| `edge_kinds` | string[] | No | Edge types to follow: calls, imports, extends, implements, exports, agent_linked |
+| `session_id` | string | No | Session ID for exploration tracking |
+
+```
+context_query({
+  query: "payment processing",
+  depth: 2,
+  session_id: "debug-checkout"
+})
+```
+
+Returns each search result plus its graph neighbors — callers, callees, imports, and inheritance — without reading additional files.
+
+### Tool: graph_annotate
+
+Leave notes on code nodes and create links between related chunks.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `session_id` | string | Yes | Session ID |
+| `node_id` | string | Yes | Chunk ID to annotate |
+| `note` | string | No | Note to attach |
+| `link_to` | string[] | No | Chunk IDs to create agent_linked edges to |
+| `reasoning` | string | No | Reasoning log entry |
+
+### Tool: session_summary
+
+View exploration state: visited nodes, frontier, annotations, reasoning log, and graph stats.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `session_id` | string | Yes | Session ID to summarize |
+
+### Graph Configuration
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `SEMANTIC_CODE_GRAPH_ENABLED` | Enable the context graph | `false` |
+| `SEMANTIC_CODE_GRAPH_DEPTH` | Default BFS traversal depth (1-5) | `2` |
+| `SEMANTIC_CODE_SESSION_TTL` | Session TTL in seconds | `3600` |
+| `SEMANTIC_CODE_EDGE_KINDS` | Comma-separated edge types to follow | all types |
+
+The graph degrades gracefully — if SQLite initialization fails, semantic search continues to work without graph features.
+
 ## Supported Languages
 
 - TypeScript / JavaScript (including TSX/JSX)
@@ -155,6 +223,10 @@ Other languages fall back to line-based chunking.
 |----------|-------------|---------|
 | `SEMANTIC_CODE_ROOT` | Root directory to index | Current working directory |
 | `SEMANTIC_CODE_INDEX` | Custom index storage location | `.semantic-code/index/` |
+| `SEMANTIC_CODE_GRAPH_ENABLED` | Enable context graph | `false` |
+| `SEMANTIC_CODE_GRAPH_DEPTH` | Default graph traversal depth (1-5) | `2` |
+| `SEMANTIC_CODE_SESSION_TTL` | Session TTL in seconds | `3600` |
+| `SEMANTIC_CODE_EDGE_KINDS` | Edge types to follow (comma-separated) | all types |
 
 ### Default Ignore Patterns
 
@@ -194,6 +266,7 @@ Invalid inputs throw typed errors (`InvalidFilterError`, `PathTraversalError`, `
 ## Storage
 
 - Index location: `.semantic-code/index/` (add to `.gitignore`)
+- Graph database: `.semantic-code/index/graph.db` (SQLite, created when graph is enabled)
 - Model cache: `~/.cache/semantic-code-mcp/`
 - Estimated size: 3GB codebase → ~1.5GB index (with float16)
 
@@ -231,21 +304,35 @@ semantic-code-mcp/
 ├── src/
 │   ├── index.ts              # MCP server entry point
 │   ├── chunker/
-│   │   ├── index.ts          # Main chunker logic
+│   │   ├── index.ts          # AST-aware chunker + edge extraction
 │   │   ├── languages.ts      # Language configs with WASM paths
 │   │   └── wasm-loader.ts    # WASM grammar loader with caching
 │   ├── embedder/
 │   │   ├── index.ts          # ONNX embedding generation
 │   │   └── model.ts          # Model download & loading
+│   ├── graph/
+│   │   ├── index.ts          # SQLite graph store (nodes, edges, BFS)
+│   │   ├── config.ts         # Graph configuration from env vars
+│   │   ├── extractor.ts      # Edge resolution (raw edges → graph edges)
+│   │   ├── schema.ts         # SQLite DDL for graph tables
+│   │   ├── session.ts        # In-memory session manager
+│   │   └── types.ts          # GraphNode, GraphEdge, RawEdge types
 │   ├── store/
 │   │   └── index.ts          # LanceDB integration
 │   ├── search/
 │   │   ├── index.ts          # Hybrid search orchestration
 │   │   └── reranker.ts       # Cross-encoder reranking
 │   ├── watcher/
 │   │   └── index.ts          # File watcher + incremental indexing
-│   └── tools/
-│       └── semantic-search.ts # MCP tool definition
+│   ├── tools/
+│   │   ├── semantic-search.ts # semantic_search tool
+│   │   ├── context-query.ts   # context_query tool (search + graph)
+│   │   ├── graph-annotate.ts  # graph_annotate tool
+│   │   └── session-summary.ts # session_summary tool
+│   └── utils/
+│       ├── logger.ts          # Structured logging
+│       ├── validation.ts      # Shared ID validation
+│       └── ...
 ├── grammars/                  # Pre-built WASM parsers
 ├── scripts/
 │   └── copy-grammars.js      # Build script for WASM files

docs/architecture.md

@@ -56,8 +56,19 @@ This document describes the internal architecture of semantic-code-mcp.
               │                       │
               │ - Tree-sitter parsing │
               │ - Semantic splitting  │
+              │ - Edge extraction     │
               │ - Fallback chunking   │
               └───────────────────────┘
+
+              ┌───────────────────────┐
+              │    Context Graph      │
+              │     (graph/)          │
+              │                       │
+              │ - SQLite graph store  │
+              │ - BFS traversal       │
+              │ - Session memory      │
+              │ - Edge resolution     │
+              └───────────────────────┘
 ```
 
 ## Component Details
@@ -66,9 +77,10 @@ This document describes the internal architecture of semantic-code-mcp.
 
 The entry point that implements the Model Context Protocol:
 
-- Registers the `semantic_search` tool
+- Registers `semantic_search`, `context_query`, `graph_annotate`, and `session_summary` tools
 - Handles JSON-RPC communication over stdio
 - Manages server lifecycle
+- Conditionally initializes the context graph when `SEMANTIC_CODE_GRAPH_ENABLED=true`
 
 ### 2. SemanticSearchTool (`src/tools/semantic-search.ts`)
 
@@ -185,6 +197,37 @@ File Change → Debounce (1s) → Read Content → Check Hash → Chunk → Embe
 - Debouncing to avoid excessive re-indexing
 - Graceful shutdown with pending operation tracking
 
+### 8. Context Graph (`src/graph/`)
+
+Opt-in structural awareness layer using SQLite (better-sqlite3):
+
+**Components:**
+- **GraphStore** (`index.ts`): SQLite-backed store for nodes and edges with BFS traversal
+- **Extractor** (`extractor.ts`): Resolves raw edges (symbol names) to concrete graph edges (chunk IDs)
+- **SessionManager** (`session.ts`): In-memory session state with TTL-based cleanup
+- **Config** (`config.ts`): Environment variable parsing for graph settings
+
+**Edge Types:**
+- `calls` — function/method call relationships
+- `imports` — import/require dependencies
+- `extends` — class inheritance
+- `implements` — interface implementation
+- `exports` — module exports
+- `agent_linked` — agent-created links via `graph_annotate`
+
+**Schema (SQLite):**
+```
+graph_nodes: id, file_path, symbol_name, kind, start_line, end_line, updated_at, stale
+graph_edges: source_id, target_id, edge_type, weight, metadata
+graph_meta:  key, value
+```
+
+**Design Decisions:**
+- SQLite for graph traversal (BFS < 1ms), separate from LanceDB for vectors
+- In-memory sessions (ephemeral by design, tied to agent tasks not codebase)
+- Graceful degradation: graph failure never breaks semantic search
+- ID validation via shared `utils/validation.ts` for defense-in-depth
+
 ## Data Flow
 
 ### Indexing Flow

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@smallthinkingmachines/semantic-code-mcp",
-  "version": "0.3.3",
+  "version": "0.4.0",
   "description": "MCP server for semantic code search using AST-aware chunking and vector embeddings",
   "type": "module",
   "main": "dist/index.js",
@@ -35,6 +35,8 @@
     "semantic-search",
     "mcp-server",
     "code-understanding",
+    "code-graph",
+    "context-graph",
     "vector-search",
     "ai-coding",
     "claude-code",